Mon Jan 10 03:28:33 UTC 2022 I: starting to build salmon/bullseye/amd64 on jenkins on '2022-01-10 03:28' Mon Jan 10 03:28:33 UTC 2022 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_14/22365/console.log Mon Jan 10 03:28:33 UTC 2022 I: Downloading source for bullseye/salmon=1.4.0+ds1-1 --2022-01-10 03:28:34-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/salmon/salmon_1.4.0%2bds1-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2518 (2.5K) Saving to: ‘salmon_1.4.0+ds1-1.dsc’ 0K .. 100% 9.37M=0s 2022-01-10 03:28:34 (9.37 MB/s) - ‘salmon_1.4.0+ds1-1.dsc’ saved [2518/2518] Mon Jan 10 03:28:34 UTC 2022 I: salmon_1.4.0+ds1-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: salmon Binary: salmon Architecture: any-amd64 arm64 Version: 1.4.0+ds1-1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Kevin Murray Homepage: https://github.com/COMBINE-lab/salmon Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/salmon Vcs-Git: https://salsa.debian.org/med-team/salmon.git Build-Depends: debhelper-compat (= 13), cmake, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev, libboost-thread-dev, libboost-program-options-dev, libboost-timer-dev, libjellyfish-2.0-dev (>> 2.2.3-2), libpthread-stubs0-dev, libsparsehash-dev, libdivsufsort-dev, libbwa-dev, pkg-config, libjemalloc-dev, libcereal-dev, libtbb-dev, libgff-dev (>> 2.0), libstaden-read-dev, libspdlog-dev, libtclap-dev, help2man, sphinx-doc, python3-sphinx, python3-sphinx-rtd-theme, zlib1g-dev, libeigen3-dev, libbz2-dev, liblzma-dev, rapmap-dev, libsimde-dev Package-List: salmon deb science optional arch=any-amd64,arm64 Checksums-Sha1: c14a970370420fdb5d177cff7fc4bb753b80b5a5 5608704 salmon_1.4.0+ds1.orig.tar.xz b7ec3a29866b53f5395c9eebba3111d31dd9b6ca 976308 salmon_1.4.0+ds1-1.debian.tar.xz Checksums-Sha256: 741f40cdf559fa08bd3ae30196a77a6ccef80b149d1c0d327349f4ae89b820d8 5608704 salmon_1.4.0+ds1.orig.tar.xz 7b64fe328ea05b20c2369be5860a2363bcb108e7a91cdc461d41ebe0203cbf62 976308 salmon_1.4.0+ds1-1.debian.tar.xz Files: 22090df4890b423fa244b653ea40ab41 5608704 salmon_1.4.0+ds1.orig.tar.xz 33cffafe0ef04caf1ffa6e2a490894b6 976308 salmon_1.4.0+ds1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl+/9TkACgkQPCZ2P2xn 5uKs1w/7BOKNuzMV1xc0c1zOD+edV0/HHdF5JSfQCIqQNF8C0ucBrY1ZCoS/Q04Y pUAF3oPdpqyad1n4uQG6gvu+j4oJX2P1nxMfck5QAJs1VR6YVXMV/DmPdXM5/9Pp VAzf50dCtdzUfGZdCX3T20d6wrXyc6nCDB6p1mKUuQmotxoX1Ti4PqVUqBZxJKqx IIn5ewdzKTiFs6Jj+GCtE6XDR9lsQBqXXOCjQToDlAdcqD08EzEfN44MpsF+z0Pa OA0SM69TUPQsHpjZksvk5Ze8gouZYX81g4aeS0ZKNp/rvFYQyz8/WFYfprxd0+hV DEkdkb3cfmSA90Mi2vfg35Xe3AiN8fIsT4UO6drAKufd78yKZb5su8UDj2ZOaKwQ 3npvBsIO2+kHhWA7ToqINjJOgD//ZQbVqGpeY5kq8Ez4DgpbE8zBJQ+9OAftuGLQ xsrzDXsXQDYXhsnAIrRTigDz7x+14bysJMKsdo7JkfE37sfVTllhpJ+F0AQ+VE71 vE8NYwxTPhhYjEhShalJDLSr4LHWiOHxyD+4u9nfxzajLCTPLESV6KKQjDcrGY+R CcJdxXyhrYPMCQ8gBVqKRT19DNSCHc4gNYXeODh7LnuUl4xUNIhRp6K77lMufXQJ cBYfAyXvzgmZ8fhtYVWJDimxsqNaFcRbm30TPzPxZczwO5f4N0g= =SkrK -----END PGP SIGNATURE----- Mon Jan 10 03:28:34 UTC 2022 I: Checking whether the package is not for us Mon Jan 10 03:28:34 UTC 2022 I: Starting 1st build on remote node ionos5-amd64.debian.net. Mon Jan 10 03:28:34 UTC 2022 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Mon Jan 10 03:39:07 UTC 2022 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Feb 11 21:51:38 -12 2023 I: pbuilder-time-stamp: 1676195498 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [salmon_1.4.0+ds1-1.dsc] I: copying [./salmon_1.4.0+ds1.orig.tar.xz] I: copying [./salmon_1.4.0+ds1-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.Gr4G7WXy/trustedkeys.kbx': General error gpgv: Signature made Thu Nov 26 06:34:33 2020 -12 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./salmon_1.4.0+ds1-1.dsc dpkg-source: info: extracting salmon in salmon-1.4.0+ds1 dpkg-source: info: unpacking salmon_1.4.0+ds1.orig.tar.xz dpkg-source: info: unpacking salmon_1.4.0+ds1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying pufferfish dpkg-source: info: applying disable-version-check.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2512877/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='fe0a9dc239554410af99c4bfc096d523' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2512877' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.VLIak0ug0A/pbuilderrc_pcdY --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.VLIak0ug0A/b1 --logfile b1/build.log salmon_1.4.0+ds1-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 4 2021 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jul 28 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 28 2021 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jul 28 2021 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 28 2021 more -rwsr-xr-x 1 root root 55528 Jul 28 2021 mount -rwxr-xr-x 1 root root 18664 Jul 28 2021 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Feb 9 03:46 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jul 28 2021 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 28 2021 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 28 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/2512877/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cmake, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev, libboost-thread-dev, libboost-program-options-dev, libboost-timer-dev, libjellyfish-2.0-dev (>> 2.2.3-2), libpthread-stubs0-dev, libsparsehash-dev, libdivsufsort-dev, libbwa-dev, pkg-config, libjemalloc-dev, libcereal-dev, libtbb-dev, libgff-dev (>> 2.0), libstaden-read-dev, libspdlog-dev, libtclap-dev, help2man, sphinx-doc, python3-sphinx, python3-sphinx-rtd-theme, zlib1g-dev, libeigen3-dev, libbz2-dev, liblzma-dev, rapmap-dev, libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19655 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libboost-filesystem-dev; however: Package libboost-filesystem-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-system-dev; however: Package libboost-system-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-thread-dev; however: Package libboost-thread-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-timer-dev; however: Package libboost-timer-dev is not installed. pbuilder-satisfydepends-dummy depends on libjellyfish-2.0-dev (>> 2.2.3-2); however: Package libjellyfish-2.0-dev is not installed. pbuilder-satisfydepends-dummy depends on libpthread-stubs0-dev; however: Package libpthread-stubs0-dev is not installed. pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however: Package libsparsehash-dev is not installed. pbuilder-satisfydepends-dummy depends on libdivsufsort-dev; however: Package libdivsufsort-dev is not installed. pbuilder-satisfydepends-dummy depends on libbwa-dev; however: Package libbwa-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libjemalloc-dev; however: Package libjemalloc-dev is not installed. pbuilder-satisfydepends-dummy depends on libcereal-dev; however: Package libcereal-dev is not installed. pbuilder-satisfydepends-dummy depends on libtbb-dev; however: Package libtbb-dev is not installed. pbuilder-satisfydepends-dummy depends on libgff-dev (>> 2.0); however: Package libgff-dev is not installed. pbuilder-satisfydepends-dummy depends on libstaden-read-dev; however: Package libstaden-read-dev is not installed. pbuilder-satisfydepends-dummy depends on libspdlog-dev; however: Package libspdlog-dev is not installed. pbuilder-satisfydepends-dummy depends on libtclap-dev; however: Package libtclap-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on sphinx-doc; however: Package sphinx-doc is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however: Package python3-sphinx-rtd-theme is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on rapmap-dev; however: Package rapmap-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docutils-common{a} docutils-doc{a} dwz{a} file{a} fonts-font-awesome{a} fonts-lato{a} fonts-mathjax{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libboost-atomic1.74-dev{a} libboost-atomic1.74.0{a} libboost-chrono1.74-dev{a} libboost-chrono1.74.0{a} libboost-date-time1.74-dev{a} libboost-date-time1.74.0{a} libboost-filesystem-dev{a} libboost-filesystem1.74-dev{a} libboost-filesystem1.74.0{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-serialization1.74-dev{a} libboost-serialization1.74.0{a} libboost-system-dev{a} libboost-system1.74-dev{a} libboost-system1.74.0{a} libboost-thread-dev{a} libboost-thread1.74-dev{a} libboost-thread1.74.0{a} libboost-timer-dev{a} libboost-timer1.74-dev{a} libboost-timer1.74.0{a} libboost1.74-dev{a} libbrotli1{a} libbwa-dev{a} libbz2-dev{a} libcereal-dev{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdivsufsort-dev{a} libdivsufsort3{a} libeigen3-dev{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfmt-dev{a} libfmt7{a} libgff-dev{a} libglib2.0-0{a} libhtscodecs-dev{a} libhtscodecs2{a} libicu-dev{a} libicu67{a} libjellyfish-2.0-2{a} libjellyfish-2.0-dev{a} libjemalloc-dev{a} libjemalloc2{a} libjs-jquery{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp24{a} libldap-2.4-2{a} liblocale-gettext-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmpdec3{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libprocps8{a} libpsl5{a} libpthread-stubs0-dev{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsimde-dev{a} libsparsehash-dev{a} libspdlog-dev{a} libspdlog1{a} libssh2-1{a} libstaden-read-dev{a} libstaden-read14{a} libsub-override-perl{a} libtbb-dev{a} libtbb2{a} libtclap-dev{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} media-types{a} openssl{a} pkg-config{a} po-debconf{a} procps{a} python-babel-localedata{a} python-requests-doc{a} python3{a} python3-alabaster{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-distutils{a} python3-doc{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-lib2to3{a} python3-markupsafe{a} python3-minimal{a} python3-packaging{a} python3-pkg-resources{a} python3-pygments{a} python3-pyparsing{a} python3-requests{a} python3-roman{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-tz{a} python3-urllib3{a} python3.9{a} python3.9-doc{a} python3.9-minimal{a} rapidjson-dev{a} rapmap-dev{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-doc{a} sphinx-rtd-theme-common{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl javascript-common libarchive-cpio-perl libglib2.0-data libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx psmisc publicsuffix python3-pil shared-mime-info wget xdg-user-dirs 0 packages upgraded, 169 newly installed, 0 to remove and 0 not upgraded. Need to get 106 MB of archives. After unpacking 592 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 fonts-lato all 2.0-2.1 [2696 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 liblocale-gettext-perl amd64 1.07-4+b1 [19.0 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 sgml-base all 1.30 [15.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2 [102 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1k-1+deb11u1 [851 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 cmake-data all 3.18.4-2+deb11u1 [1725 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libarchive13 amd64 3.4.3-2+b1 [343 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3 [232 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u1 [341 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libjsoncpp24 amd64 1.9.4-4 [78.9 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 librhash0 amd64 1.4.1-2 [129 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 libuv1 amd64 1.40.0-2 [132 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 cmake amd64 3.18.4-2+deb11u1 [5593 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 docutils-common all 0.16+dfsg-4 [129 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 docutils-doc all 0.16+dfsg-4 [932 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 help2man amd64 1.48.1 [190 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 icu-devtools amd64 67.1-7 [201 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libboost1.74-dev amd64 1.74.0-9 [9534 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libboost-atomic1.74.0 amd64 1.74.0-9 [244 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libboost-atomic1.74-dev amd64 1.74.0-9 [245 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libboost-chrono1.74.0 amd64 1.74.0-9 [252 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libboost-chrono1.74-dev amd64 1.74.0-9 [260 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libboost-date-time1.74.0 amd64 1.74.0-9 [241 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 libboost-serialization1.74.0 amd64 1.74.0-9 [340 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 libboost-serialization1.74-dev amd64 1.74.0-9 [383 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libboost-date-time1.74-dev amd64 1.74.0-9 [250 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libboost-filesystem1.74.0 amd64 1.74.0-9 [283 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libboost-system1.74.0 amd64 1.74.0-9 [241 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 libboost-system1.74-dev amd64 1.74.0-9 [243 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libboost-filesystem1.74-dev amd64 1.74.0-9 [304 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 libboost-filesystem-dev amd64 1.74.0.3 [4368 B] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libboost-regex1.74.0 amd64 1.74.0-9 [516 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 libicu-dev amd64 67.1-7 [9597 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libboost-regex1.74-dev amd64 1.74.0-9 [588 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 libboost-iostreams1.74-dev amd64 1.74.0-9 [273 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 libboost-iostreams-dev amd64 1.74.0.3 [4316 B] Get: 93 http://deb.debian.org/debian bullseye/main amd64 libboost-program-options1.74.0 amd64 1.74.0-9 [356 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 libboost-program-options1.74-dev amd64 1.74.0-9 [386 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 libboost-program-options-dev amd64 1.74.0.3 [4340 B] Get: 96 http://deb.debian.org/debian bullseye/main amd64 libboost-system-dev amd64 1.74.0.3 [4468 B] Get: 97 http://deb.debian.org/debian bullseye/main amd64 libboost-thread1.74.0 amd64 1.74.0-9 [279 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 libboost-thread1.74-dev amd64 1.74.0-9 [290 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 libboost-thread-dev amd64 1.74.0.3 [4356 B] Get: 100 http://deb.debian.org/debian bullseye/main amd64 libboost-timer1.74.0 amd64 1.74.0-9 [250 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 libboost-timer1.74-dev amd64 1.74.0-9 [254 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 libboost-timer-dev amd64 1.74.0.3 [4456 B] Get: 103 http://deb.debian.org/debian bullseye/main amd64 libbwa-dev amd64 0.7.17-6+b1 [143 kB] Get: 104 http://deb.debian.org/debian bullseye/main amd64 libbz2-dev amd64 1.0.8-4 [30.1 kB] Get: 105 http://deb.debian.org/debian bullseye/main amd64 rapidjson-dev all 1.1.0+dfsg2-7 [98.9 kB] Get: 106 http://deb.debian.org/debian bullseye/main amd64 libcereal-dev all 1.3.0+dfsg-1 [210 kB] Get: 107 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u1 [338 kB] Get: 108 http://deb.debian.org/debian bullseye/main amd64 libcurl4-gnutls-dev amd64 7.74.0-1.3+deb11u1 [429 kB] Get: 109 http://deb.debian.org/debian bullseye/main amd64 libdivsufsort3 amd64 2.0.1-5 [44.7 kB] Get: 110 http://deb.debian.org/debian bullseye/main amd64 libdivsufsort-dev amd64 2.0.1-5 [19.1 kB] Get: 111 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1 [1370 kB] Get: 112 http://deb.debian.org/debian bullseye/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] Get: 113 http://deb.debian.org/debian bullseye/main amd64 libeigen3-dev all 3.3.9-2 [858 kB] Get: 114 http://deb.debian.org/debian bullseye/main amd64 libfmt7 amd64 7.1.3+ds1-5 [110 kB] Get: 115 http://deb.debian.org/debian bullseye/main amd64 libfmt-dev amd64 7.1.3+ds1-5 [142 kB] Get: 116 http://deb.debian.org/debian bullseye/main amd64 libgff-dev amd64 2.0.0-1 [153 kB] Get: 117 http://deb.debian.org/debian bullseye/main amd64 libhtscodecs2 amd64 0.5-3 [50.6 kB] Get: 118 http://deb.debian.org/debian bullseye/main amd64 libhtscodecs-dev amd64 0.5-3 [2518 kB] Get: 119 http://deb.debian.org/debian bullseye/main amd64 libjellyfish-2.0-2 amd64 2.3.0-10 [65.1 kB] Get: 120 http://deb.debian.org/debian bullseye/main amd64 libjellyfish-2.0-dev amd64 2.3.0-10 [138 kB] Get: 121 http://deb.debian.org/debian bullseye/main amd64 libjemalloc2 amd64 5.2.1-3 [248 kB] Get: 122 http://deb.debian.org/debian bullseye/main amd64 libjemalloc-dev amd64 5.2.1-3 [437 kB] Get: 123 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 124 http://deb.debian.org/debian bullseye/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 125 http://deb.debian.org/debian bullseye/main amd64 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 126 http://deb.debian.org/debian bullseye/main amd64 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 127 http://deb.debian.org/debian bullseye/main amd64 liblzma-dev amd64 5.2.5-2 [229 kB] Get: 128 http://deb.debian.org/debian bullseye/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B] Get: 129 http://deb.debian.org/debian bullseye/main amd64 libsimde-dev all 0.7.2-4 [259 kB] Get: 130 http://deb.debian.org/debian bullseye/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 131 http://deb.debian.org/debian bullseye/main amd64 libspdlog1 amd64 1:1.8.1+ds-2.1 [89.7 kB] Get: 132 http://deb.debian.org/debian bullseye/main amd64 libspdlog-dev amd64 1:1.8.1+ds-2.1 [177 kB] Get: 133 http://deb.debian.org/debian bullseye/main amd64 libstaden-read14 amd64 1.14.13-4 [265 kB] Get: 134 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get: 135 http://deb.debian.org/debian bullseye/main amd64 libstaden-read-dev amd64 1.14.13-4 [343 kB] Get: 136 http://deb.debian.org/debian bullseye/main amd64 libtbb2 amd64 2020.3-1 [161 kB] Get: 137 http://deb.debian.org/debian bullseye/main amd64 libtbb-dev amd64 2020.3-1 [313 kB] Get: 138 http://deb.debian.org/debian bullseye/main amd64 libtclap-dev amd64 1.2.3-1 [143 kB] Get: 139 http://deb.debian.org/debian bullseye/main amd64 python-babel-localedata all 2.8.0+dfsg.1-7 [4997 kB] Get: 140 http://deb.debian.org/debian bullseye/main amd64 python-requests-doc all 2.25.1+dfsg-2 [195 kB] Get: 141 http://deb.debian.org/debian bullseye/main amd64 python3-alabaster all 0.7.8-1.1 [18.6 kB] Get: 142 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 143 http://deb.debian.org/debian bullseye/main amd64 python3-tz all 2021.1-1 [34.8 kB] Get: 144 http://deb.debian.org/debian bullseye/main amd64 python3-babel all 2.8.0+dfsg.1-7 [100 kB] Get: 145 http://deb.debian.org/debian bullseye/main amd64 python3-certifi all 2020.6.20-1 [151 kB] Get: 146 http://deb.debian.org/debian bullseye/main amd64 python3-chardet all 4.0.0-1 [99.0 kB] Get: 147 http://deb.debian.org/debian bullseye/main amd64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 148 http://deb.debian.org/debian bullseye/main amd64 python3-distutils all 3.9.2-1 [143 kB] Get: 149 http://deb.debian.org/debian bullseye/main amd64 python3.9-doc all 3.9.2-1 [10.9 MB] Get: 150 http://deb.debian.org/debian bullseye/main amd64 python3-doc all 3.9.2-3 [21.6 kB] Get: 151 http://deb.debian.org/debian bullseye/main amd64 python3-roman all 2.0.0-5 [9064 B] Get: 152 http://deb.debian.org/debian bullseye/main amd64 python3-docutils all 0.16+dfsg-4 [384 kB] Get: 153 http://deb.debian.org/debian bullseye/main amd64 python3-idna all 2.10-1 [37.4 kB] Get: 154 http://deb.debian.org/debian bullseye/main amd64 python3-imagesize all 1.2.0-2 [5824 B] Get: 155 http://deb.debian.org/debian bullseye/main amd64 python3-markupsafe amd64 1.1.1-1+b3 [15.2 kB] Get: 156 http://deb.debian.org/debian bullseye/main amd64 python3-jinja2 all 2.11.3-1 [114 kB] Get: 157 http://deb.debian.org/debian bullseye/main amd64 python3-pyparsing all 2.4.7-1 [109 kB] Get: 158 http://deb.debian.org/debian bullseye/main amd64 python3-packaging all 20.9-2 [33.5 kB] Get: 159 http://deb.debian.org/debian bullseye/main amd64 python3-pygments all 2.7.1+dfsg-2.1 [657 kB] Get: 160 http://deb.debian.org/debian bullseye/main amd64 python3-six all 1.16.0-2 [17.5 kB] Get: 161 http://deb.debian.org/debian bullseye/main amd64 python3-urllib3 all 1.26.5-1~exp1 [114 kB] Get: 162 http://deb.debian.org/debian bullseye/main amd64 python3-requests all 2.25.1+dfsg-2 [69.3 kB] Get: 163 http://deb.debian.org/debian bullseye/main amd64 python3-snowballstemmer all 2.1.0-1 [58.7 kB] Get: 164 http://deb.debian.org/debian bullseye/main amd64 sphinx-common all 3.4.3-2 [578 kB] Get: 165 http://deb.debian.org/debian bullseye/main amd64 python3-sphinx all 3.4.3-2 [545 kB] Get: 166 http://deb.debian.org/debian bullseye/main amd64 sphinx-rtd-theme-common all 0.5.1+dfsg-1 [995 kB] Get: 167 http://deb.debian.org/debian bullseye/main amd64 python3-sphinx-rtd-theme all 0.5.1+dfsg-1 [20.9 kB] Get: 168 http://deb.debian.org/debian bullseye/main amd64 rapmap-dev all 0.15.0+dfsg-1 [194 kB] Get: 169 http://deb.debian.org/debian bullseye/main amd64 sphinx-doc all 3.4.3-2 [1971 kB] Fetched 106 MB in 1s (95.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. 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Setting up libdivsufsort3:amd64 (2.0.1-5) ... Setting up openssl (1.1.1k-1+deb11u1) ... Setting up libelf1:amd64 (0.183-1) ... Setting up rapmap-dev (0.15.0+dfsg-1) ... Setting up readline-common (8.1-1) ... Setting up libboost-timer1.74.0:amd64 (1.74.0-9) ... Setting up libicu-dev:amd64 (67.1-7) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (0.5.1+dfsg-1) ... Setting up libboost-filesystem-dev:amd64 (1.74.0.3) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libprocps8:amd64 (2:3.3.17-5) ... Setting up libjs-underscore (1.9.1~dfsg-3) ... Setting up libboost-thread1.74.0:amd64 (1.74.0-9) ... Setting up libdivsufsort-dev:amd64 (2.0.1-5) ... Setting up libbz2-dev:amd64 (1.0.8-4) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libjellyfish-2.0-dev:amd64 (2.3.0-10) ... Setting up libtool (2.4.6-15) ... Setting up libarchive13:amd64 (3.4.3-2+b1) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libboost-system-dev:amd64 (1.74.0.3) ... Setting up libcereal-dev (1.3.0+dfsg-1) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u1) ... Setting up libcurl4-gnutls-dev:amd64 (7.74.0-1.3+deb11u1) ... Setting up python3.9-doc (3.9.2-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.1) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libeigen3-dev (3.3.9-2) ... Setting up libboost-timer1.74-dev:amd64 (1.74.0-9) ... Setting up libfmt-dev:amd64 (7.1.3+ds1-5) ... Setting up libjs-sphinxdoc (3.4.3-2) ... Setting up python-requests-doc (2.25.1+dfsg-2) ... Setting up autoconf (2.69-14) ... Setting up libboost-serialization1.74-dev:amd64 (1.74.0-9) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up libboost-regex1.74-dev:amd64 (1.74.0-9) ... Setting up groff-base (1.22.4-6) ... Setting up xml-core (0.18+nmu1) ... Setting up procps (2:3.3.17-5) ... Setting up libcurl4:amd64 (7.74.0-1.3+deb11u1) ... Setting up libstaden-read14:amd64 (1.14.13-4) ... Setting up libboost-timer-dev:amd64 (1.74.0.3) ... Setting up python3-doc (3.9.2-3) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up sphinx-doc (3.4.3-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libstaden-read-dev (1.14.13-4) ... Setting up libspdlog-dev:amd64 (1:1.8.1+ds-2.1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libboost-iostreams1.74-dev:amd64 (1.74.0-9) ... Setting up dh-autoreconf (20) ... Setting up libboost-date-time1.74-dev:amd64 (1.74.0-9) ... Setting up sphinx-common (3.4.3-2) ... Setting up cmake (3.18.4-2+deb11u1) ... Setting up libboost-thread1.74-dev:amd64 (1.74.0-9) ... Setting up python3.9 (3.9.2-1) ... Setting up libboost-thread-dev:amd64 (1.74.0.3) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up libboost-iostreams-dev:amd64 (1.74.0.3) ... Setting up python3-markupsafe (1.1.1-1+b3) ... Setting up python3-tz (2021.1-1) ... Setting up python3-six (1.16.0-2) ... Setting up python3-roman (2.0.0-5) ... Setting up python3-jinja2 (2.11.3-1) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-certifi (2020.6.20-1) ... Setting up python3-snowballstemmer (2.1.0-1) ... Setting up python3-idna (2.10-1) ... Setting up python3-urllib3 (1.26.5-1~exp1) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-imagesize (1.2.0-2) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-distutils (3.9.2-1) ... Setting up python3-babel (2.8.0+dfsg.1-7) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-alabaster (0.7.8-1.1) ... Setting up python3-pygments (2.7.1+dfsg-2.1) ... Setting up python3-packaging (20.9-2) ... Setting up python3-chardet (4.0.0-1) ... Setting up python3-requests (2.25.1+dfsg-2) ... Processing triggers for libc-bin (2.31-13+deb11u2) ... Processing triggers for sgml-base (1.30) ... Setting up docutils-common (0.16+dfsg-4) ... Processing triggers for sgml-base (1.30) ... Setting up python3-docutils (0.16+dfsg-4) ... update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python3-sphinx (3.4.3-2) ... Setting up python3-sphinx-rtd-theme (0.5.1+dfsg-1) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/salmon-1.4.0+ds1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../salmon_1.4.0+ds1-1_source.changes dpkg-buildpackage: info: source package salmon dpkg-buildpackage: info: source version 1.4.0+ds1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with sphinxdoc debian/rules override_dh_auto_clean make[1]: Entering directory '/build/salmon-1.4.0+ds1' dh_auto_clean rm -rf external rm -f debian/*.1 rm -Rf sample_data cd doc && /usr/bin/make clean make[2]: Entering directory '/build/salmon-1.4.0+ds1/doc' rm -rf build/* make[2]: Leaving directory '/build/salmon-1.4.0+ds1/doc' rm -rf tests/unitTests make[1]: Leaving directory '/build/salmon-1.4.0+ds1' dh_clean debian/rules binary dh binary --with sphinxdoc dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/salmon-1.4.0+ds1' # See here # https://github.com/COMBINE-lab/salmon/issues/87 # for a discussion with upstream why it is necessary to include rapmap source mkdir -p /build/salmon-1.4.0+ds1/external/install/src/rapmap cp -av /usr/share/rapmap/src/* /build/salmon-1.4.0+ds1/external/install/src/rapmap '/usr/share/rapmap/src/HitManager.cpp' -> '/build/salmon-1.4.0+ds1/external/install/src/rapmap/HitManager.cpp' '/usr/share/rapmap/src/RapMapFileSystem.cpp' -> '/build/salmon-1.4.0+ds1/external/install/src/rapmap/RapMapFileSystem.cpp' '/usr/share/rapmap/src/RapMapSAIndex.cpp' -> '/build/salmon-1.4.0+ds1/external/install/src/rapmap/RapMapSAIndex.cpp' '/usr/share/rapmap/src/RapMapSAIndexer.cpp' -> '/build/salmon-1.4.0+ds1/external/install/src/rapmap/RapMapSAIndexer.cpp' '/usr/share/rapmap/src/RapMapUtils.cpp' -> '/build/salmon-1.4.0+ds1/external/install/src/rapmap/RapMapUtils.cpp' '/usr/share/rapmap/src/bit_array.c' -> '/build/salmon-1.4.0+ds1/external/install/src/rapmap/bit_array.c' '/usr/share/rapmap/src/rank9b.cpp' -> '/build/salmon-1.4.0+ds1/external/install/src/rapmap/rank9b.cpp' dh_auto_configure -- -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DLIBLZMA_HAS_AUTO_DECODER=1 -DLIBLZMA_HAS_EASY_ENCODER=1 -DLIBLZMA_HAS_LZMA_PRESET=1 -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE -DCMAKE_BUILD_TYPE=Release -DUSE_SHARED_LIBS=TRUE cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DLIBLZMA_HAS_AUTO_DECODER=1 -DLIBLZMA_HAS_EASY_ENCODER=1 -DLIBLZMA_HAS_LZMA_PRESET=1 -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE -DCMAKE_BUILD_TYPE=Release -DUSE_SHARED_LIBS=TRUE .. CC: gcc CC version: -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done Detected non-ARM host. Setting USE_ARM to false. version: 1.4.0 -- CMAKE_BUILD_TYPE = Release -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Check if compiler accepts -pthread -- Check if compiler accepts -pthread - yes -- Found Threads: TRUE Building with CONDA_BUILD flag Making Release build setting -DHAVE_NUMERIC_LIMITS128 running cd "/build/salmon-1.4.0+ds1" && cp -r ./debian/external ./ 2>&1 -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Performing Test Iconv_IS_BUILT_IN -- Performing Test Iconv_IS_BUILT_IN - Success -- Found Iconv: /usr/lib/x86_64-linux-gnu/libc.so -- Found LibLZMA: lzma (found version "5.2.5") Found liblzma library: lzma =========================================== -- Found BZip2: -lbz2 (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found Found libbz2 library: -lbz2 =========================================== -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.59.0") found components: iostreams filesystem system timer chrono program_options BOOST_INCLUDEDIR = BOOST_LIBRARYDIR = Boost_FOUND = TRUE BOOST ROOT = BOOST INCLUDE DIR = /usr/include BOOST INCLUDE DIRS = /usr/include BOOST LIB DIR = /usr/lib/x86_64-linux-gnu BOOST LIBRARIES = Boost::iostreams;Boost::filesystem;Boost::system;Boost::timer;Boost::chrono;Boost::program_options -- Found Cereal: /usr/include -- Cereal found (include: /usr/include) FOUND SUITABLE TBB VERSION : 2020.3 TBB_LIBRARIES = -- libgff ver. 2.0.0 found. -- include: /usr/include/ -- lib : /usr/lib/ -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.74.0") -- Found libstadenio: /usr/lib/x86_64-linux-gnu/libstaden-read.so -- Staden IOLib found (include: /usr/include) -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- Found Jemalloc: /usr/lib/x86_64-linux-gnu/libjemalloc.so (found version "5.2.1-0-gea6b3e973b477b8061e0076bb257dbd7f3faa756") Found Jemalloc library --- using this memory allocator CPACK_SOURCE_IGNORE_FILES = /src/PCA.cpp;/src/PCAUtils.cpp;/build/;/scripts/AggregateToGeneLevel.py;/scripts/ExpressionTools.py;/scripts/GenerateExpressionFiles.sh;/scripts/ParseSoftFile.py;/scripts/PlotCorrelation.py;/scripts/junk;/scripts/sfstrace.log;/scripts/SFPipeline.py;/bin/;/lib/;/sample_data/;PublishREADMEToWebsite.sh;/external/;/src/obsolete/;/include/obsolete/;WebsiteHeader.txt;/experimental_configs/;.git/ CC: /usr/bin/cc CC version: version: 1.0.0 Building basic pufferfish components for salmon setting -DHAVE_NUMERIC_LIMITS128 NO_IPO = FALSE TBB_LIBRARIES = -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHED_RAPMAP -- Build files have been written to: /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/salmon-1.4.0+ds1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/salmon-1.4.0+ds1' dh_auto_build cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/salmon-1.4.0+ds1 -B/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/CMakeFiles /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build.make external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/depend make -f external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build.make external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/depend make -f external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/depend make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/depend make -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/depend make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/depend make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-1.4.0+ds1 /build/salmon-1.4.0+ds1/external/pufferfish/external/ntcard /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-1.4.0+ds1 /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/DependInfo.cmake --color= make -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/depend make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/depend make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-1.4.0+ds1 /build/salmon-1.4.0+ds1/external/pufferfish/src /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/DependInfo.cmake --color= make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/depend make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-1.4.0+ds1 /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-1.4.0+ds1 /build/salmon-1.4.0+ds1/external/pufferfish/src /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-1.4.0+ds1 /build/salmon-1.4.0+ds1/external/pufferfish/src /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-1.4.0+ds1 /build/salmon-1.4.0+ds1/src /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/alevin_core.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-1.4.0+ds1 /build/salmon-1.4.0+ds1/src /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon_core.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-1.4.0+ds1 /build/salmon-1.4.0+ds1/external/pufferfish/src /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/puffer.dir/DependInfo.cmake --color= Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/DependInfo.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/depend.internal". Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/depend.internal". Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/DependInfo.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/depend.internal". Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/depend.internal". Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/depend.internal". Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/depend.internal". Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/DependInfo.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/depend.internal". Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/depend.internal". Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/depend.internal". Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/depend.internal". Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/DependInfo.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/depend.internal". Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/depend.internal". Scanning dependencies of target ntcard Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon_core.dir/DependInfo.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon_core.dir/depend.internal". Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon_core.dir/depend.internal". Scanning dependencies of target ksw2pp_sse2 Scanning dependencies of target ksw2pp_basic Scanning dependencies of target ksw2pp_sse4 Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/alevin_core.dir/DependInfo.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/alevin_core.dir/depend.internal". Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/alevin_core.dir/depend.internal". Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/puffer.dir/DependInfo.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/puffer.dir/depend.internal". Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/puffer.dir/depend.internal". make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build.make external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build make -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' Scanning dependencies of target graphdump Scanning dependencies of target twopaco make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build.make external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build [ 1%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o [ 3%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o [ 3%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o [ 5%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o [ 5%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o [ 7%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o [ 7%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o [ 8%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o [ 9%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o [ 10%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -mno-sse4.1 -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/Common -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -std=c++14 -o CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/Common/SignalHandler.cpp [ 11%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/Common -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -std=c++14 -o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/Common/Fcontrol.cpp cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/kalloc.c cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extd.c cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -mno-sse4.1 -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -mno-sse4.1 -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/Common -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -std=c++14 -o CMakeFiles/ntcard.dir/nthll.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/nthll.cpp [ 12%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/dnachar.cpp [ 13%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/graphdump.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/../common -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/. -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/graphdump.dir/graphdump.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/graphdump.cpp Scanning dependencies of target alevin_core make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/build [ 14%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extz.c Scanning dependencies of target puffer make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 14%] Building CXX object src/CMakeFiles/alevin_core.dir/edlib.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/alevin_core.dir/edlib.cpp.o -c /build/salmon-1.4.0+ds1/src/edlib.cpp make -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/build Scanning dependencies of target salmon_core make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/build make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 15%] Building CXX object src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 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/build/salmon-1.4.0+ds1/src/jellyfish/mer_dna.cc [ 16%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishIndexer.cpp [ 16%] Building C object src/CMakeFiles/salmon_core.dir/xxhash.c.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -o CMakeFiles/salmon_core.dir/xxhash.c.o -c /build/salmon-1.4.0+ds1/src/xxhash.c cc1: warning: command-line option '-Wno-reorder' is valid for C++/ObjC++ but not for C cc1: warning: command-line option '-Wno-deprecated-copy' is valid for C++/ObjC++ but not for C [ 17%] Building CXX object src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -c /build/salmon-1.4.0+ds1/src/TranscriptGroup.cpp [ 18%] Building CXX object src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -c /build/salmon-1.4.0+ds1/src/EffectiveLengthStats.cpp [ 19%] Building CXX object src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -c /build/salmon-1.4.0+ds1/src/LibraryFormat.cpp [ 20%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_gg.c [ 21%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_gg2.c [ 22%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/twopaco.dir/constructor.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp [ 23%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_gg2_sse.c [ 23%] Building CXX object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/KSW2Aligner.cpp [ 24%] Building CXX object src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o -c /build/salmon-1.4.0+ds1/src/GenomicFeature.cpp [ 25%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/../common -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/. -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong 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-DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -c /build/salmon-1.4.0+ds1/src/VersionChecker.cpp [ 27%] Building CXX object src/CMakeFiles/salmon_core.dir/SBModel.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/SBModel.cpp.o -c /build/salmon-1.4.0+ds1/src/SBModel.cpp [ 28%] Building CXX object src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 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/build/salmon-1.4.0+ds1/src/FastxParser.cpp make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 28%] Built target ksw2pp_sse2 [ 29%] Building CXX object src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -c /build/salmon-1.4.0+ds1/src/SingleCellProtocols.cpp make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 30%] Building CXX object src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -c /build/salmon-1.4.0+ds1/src/AlevinUtils.cpp [ 30%] Built target ksw2pp_sse4 [ 31%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/concurrentbitvector.cpp [ 32%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBaseIndex.cpp In file included from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/../common/streamfastaparser.h:8, from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/graphdump.cpp:18: /usr/include/tbb/mutex.h:21:140: note: '#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ [ 33%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/../common -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/. -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.cpp [ 34%] Building CXX object src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o -c /build/salmon-1.4.0+ds1/src/StadenUtils.cpp [ 35%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -c /build/salmon-1.4.0+ds1/src/SalmonUtils.cpp In file included from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:12, from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/assemblyedgeconstructor.h:4, from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp:20: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ [ 36%] Linking CXX static library libntcard.a cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -P CMakeFiles/ntcard.dir/cmake_clean_target.cmake cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -E cmake_link_script CMakeFiles/ntcard.dir/link.txt --verbose=1 /usr/bin/ar qc libntcard.a CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o CMakeFiles/ntcard.dir/nthll.cpp.o /usr/bin/ranlib libntcard.a make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 36%] Built target ntcard [ 37%] Building CXX object src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -c /build/salmon-1.4.0+ds1/src/DistributionUtils.cpp In file included from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.h:8, from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.cpp:4: /usr/include/tbb/mutex.h:21:140: note: '#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:13, from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/assemblyedgeconstructor.h:4, from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp:20: /usr/include/tbb/mutex.h:21:140: note: '#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:14, from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/assemblyedgeconstructor.h:4, from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp:20: /usr/include/tbb/compat/thread:21:146: note: '#pragma message: TBB Warning: tbb/compat/thread is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb/compat/thread is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:19, from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/assemblyedgeconstructor.h:4, from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp:20: /usr/include/tbb/task_scheduler_init.h:21:154: note: '#pragma message: TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 37%] Built target ksw2pp_basic make -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/depend make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-1.4.0+ds1 /build/salmon-1.4.0+ds1/external/pufferfish/src /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake --color= [ 38%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/twopaco.dir/compressedstring.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/compressedstring.cpp Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/depend.internal". Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/depend.internal". Scanning dependencies of target ksw2pp make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/build make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 39%] Linking CXX static library libksw2pp.a cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake [ 40%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1 cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include 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CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o "/usr/bin/gcc-ranlib-10" libksw2pp.a make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 40%] Built target ksw2pp [ 41%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -c /build/salmon-1.4.0+ds1/src/SalmonStringUtils.cpp [ 42%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishIndex.cpp [ 43%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.cpp [ 44%] Building CXX object src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -c /build/salmon-1.4.0+ds1/src/SimplePosBias.cpp [ 45%] Building CXX object src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -c /build/salmon-1.4.0+ds1/src/SGSmooth.cpp In file included from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.h:8, from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.cpp:4: /usr/include/tbb/mutex.h:21:140: note: '#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ [ 45%] Building CXX object src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -c /build/salmon-1.4.0+ds1/external/install/src/pufferfish/metro/metrohash64.cpp [ 46%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/test.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/twopaco.dir/test.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp [ 47%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishSparseIndex.cpp [ 48%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp In file included from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:12, from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp:11: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:13, from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp:11: /usr/include/tbb/mutex.h:21:140: note: '#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:14, from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp:11: /usr/include/tbb/compat/thread:21:146: note: '#pragma message: TBB Warning: tbb/compat/thread is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb/compat/thread is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:19, from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp:11: /usr/include/tbb/task_scheduler_init.h:21:154: note: '#pragma message: TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:12, from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp:11: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ [ 48%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishLossyIndex.cpp In file included from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:13, from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp:11: /usr/include/tbb/mutex.h:21:140: note: '#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:14, from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp:11: /usr/include/tbb/compat/thread:21:146: note: '#pragma message: TBB Warning: tbb/compat/thread is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb/compat/thread is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:19, from /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp:11: /usr/include/tbb/task_scheduler_init.h:21:154: note: '#pragma message: TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1, from /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishIndexer.cpp:20: /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(spp::sparse_hashtable::dest_it) const [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; spp::sparse_hashtable::dest_it = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]': /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::value_type = std::pair > >]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3809:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hash_map::mapped_type = std::vector >]' /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:25: required from here /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >&)' is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1, from /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishIndexer.cpp:20: /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair > >; row_it = spp::sparsegroup > >, spp::libc_allocator > > > >*; col_it = std::pair > >*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator > > >]' 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1, from /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishIndexer.cpp:20: /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(spp::sparse_hashtable::dest_it) const [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >; spp::sparse_hashtable::dest_it = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >]': /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::value_type = std::pair, unsigned int>]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3809:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hash_map::mapped_type = unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:43: required from here /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >&)' is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1, from /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishIndexer.cpp:20: /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair, unsigned int>; row_it = spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*; col_it = std::pair, unsigned int>*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator, unsigned int> >]' 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ [ 49%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/edlib.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/edlib.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/edlib.cpp [ 50%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/Util.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/Util.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/Util.cpp [ 51%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9sel.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/rank9sel.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/rank9sel.cpp [ 52%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp [ 53%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9b.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/rank9b.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/rank9b.cpp [ 54%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishValidate.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishValidate.cpp [ 55%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -o CMakeFiles/twopaco.dir/common.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/common.cpp [ 56%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishStats.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishStats.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishStats.cpp [ 57%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishTestLookup.cpp [ 58%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishExamine.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishExamine.cpp [ 59%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/FastxParser.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/FastxParser.cpp [ 60%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp [ 61%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferFS.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferFS.cpp [ 62%] Building C object external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -o CMakeFiles/puffer.dir/xxhash.c.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/xxhash.c cc1: warning: command-line option '-Wno-reorder' is valid for C++/ObjC++ but not for C [ 63%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/FixFasta.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/FixFasta.cpp [ 64%] Linking CXX static library libgraphdump.a cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/cmake -P CMakeFiles/graphdump.dir/cmake_clean_target.cmake cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphdump.dir/link.txt --verbose=1 /usr/bin/ar qc libgraphdump.a CMakeFiles/graphdump.dir/graphdump.cpp.o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o /usr/bin/ranlib libgraphdump.a make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 64%] Built target graphdump [ 65%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/MemCollector.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/MemCollector.cpp In file included from /build/salmon-1.4.0+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(spp::sparse_hashtable::dest_it) const [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; spp::sparse_hashtable::dest_it = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]': /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::value_type = std::pair > >]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3809:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hash_map::mapped_type = std::vector >]' /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:25: required from here /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >&)' is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair > >; row_it = spp::sparsegroup > >, spp::libc_allocator > > > >*; col_it = std::pair > >*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator > > >]' 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(spp::sparse_hashtable::dest_it) const [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >; spp::sparse_hashtable::dest_it = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >]': /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::value_type = std::pair, unsigned int>]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3809:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hash_map::mapped_type = unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:43: required from here /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >&)' is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair, unsigned int>; row_it = spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*; col_it = std::pair, unsigned int>*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator, unsigned int> >]' 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/src/FixFasta.cpp:4: /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(spp::sparse_hashtable::dest_it) const [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; spp::sparse_hashtable::dest_it = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]': /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::value_type = std::pair > >]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3809:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hash_map::mapped_type = std::vector >]' /build/salmon-1.4.0+ds1/external/pufferfish/src/FixFasta.cpp:264:46: required from here /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >&)' is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/src/FixFasta.cpp:4: /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair > >; row_it = spp::sparsegroup > >, spp::libc_allocator > > > >*; col_it = std::pair > >*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator > > >]' 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/src/FixFasta.cpp:4: /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(spp::sparse_hashtable::dest_it) const [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >; spp::sparse_hashtable::dest_it = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >]': /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3234:9: required from 'std::pair::ne_iterator, bool> spp::sparse_hashtable::insert(P&&) [with P = std::__cxx11::basic_string&; Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; typename spp::sparsetable::ne_iterator = spp::Two_d_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::bidirectional_iterator_tag>]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:4221:73: required from 'std::pair::Identity, spp::sparse_hash_set::SetKey, EqualKey, Alloc>::const_iterator, bool> spp::sparse_hash_set::insert(P&&) [with P = std::__cxx11::basic_string&; Value = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; typename spp::sparse_hashtable::Identity, spp::sparse_hash_set::SetKey, EqualKey, Alloc>::const_iterator = spp::Two_d_iterator, const spp::sparsegroup, spp::libc_allocator > >*, const std::__cxx11::basic_string*, std::bidirectional_iterator_tag>]' /build/salmon-1.4.0+ds1/external/pufferfish/src/FixFasta.cpp:490:32: required from here /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >&)' is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/src/FixFasta.cpp:4: /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::__cxx11::basic_string; row_it = spp::sparsegroup, spp::libc_allocator > >*; col_it = std::__cxx11::basic_string*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator >]' 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ [ 65%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/MemChainer.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/MemChainer.cpp [ 66%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PuffAligner.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/PuffAligner.cpp [ 67%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishAligner.cpp [ 68%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/RefSeqConstructor.cpp [ 69%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -c /build/salmon-1.4.0+ds1/external/pufferfish/src/metro/metrohash64.cpp [ 70%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/salmon-1.4.0+ds1/external/pufferfish/include -I/build/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -c /build/salmon-1.4.0+ds1/src/LibraryFormat.cpp [ 71%] Linking CXX static library libalevin_core.a cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/alevin_core.dir/cmake_clean_target.cmake cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/alevin_core.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-10" cr libalevin_core.a CMakeFiles/alevin_core.dir/edlib.cpp.o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o "/usr/bin/gcc-ranlib-10" libalevin_core.a make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 71%] Built target alevin_core In file included from /build/salmon-1.4.0+ds1/external/pufferfish/include/RefSeqConstructor.hpp:5, from /build/salmon-1.4.0+ds1/external/pufferfish/src/RefSeqConstructor.cpp:1: /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(spp::sparse_hashtable::dest_it) const [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >; spp::sparse_hashtable::dest_it = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >]': /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::value_type = std::pair]' /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:3809:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hash_map::mapped_type = pufferfish::util::ContigBlock]' /build/salmon-1.4.0+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from 'Task RefSeqConstructor::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string]' /build/salmon-1.4.0+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >&)' is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ In file included from /build/salmon-1.4.0+ds1/external/pufferfish/include/RefSeqConstructor.hpp:5, from /build/salmon-1.4.0+ds1/external/pufferfish/src/RefSeqConstructor.cpp:1: /build/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair; row_it = spp::sparsegroup, spp::libc_allocator > >*; col_it = std::pair*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator >]' 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ [ 72%] Linking CXX static library libsalmon_core.a cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/salmon_core.dir/cmake_clean_target.cmake cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon_core.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-10" cr libsalmon_core.a CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o CMakeFiles/salmon_core.dir/xxhash.c.o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o CMakeFiles/salmon_core.dir/SBModel.cpp.o CMakeFiles/salmon_core.dir/FastxParser.cpp.o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o "/usr/bin/gcc-ranlib-10" libsalmon_core.a make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 72%] Built target salmon_core make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/depend make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-1.4.0+ds1 /build/salmon-1.4.0+ds1/src /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/unitTests.dir/DependInfo.cmake --color= Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/unitTests.dir/DependInfo.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/unitTests.dir/depend.internal". Dependee "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/unitTests.dir/depend.internal". Scanning dependencies of target unitTests make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/build make[4]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 73%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/UnitTests.cpp.o [ 75%] Building CXX object src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o [ 75%] Building CXX object src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -pthread -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/unitTests.dir/__/tests/UnitTests.cpp.o -c /build/salmon-1.4.0+ds1/tests/UnitTests.cpp cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -pthread -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -c /build/salmon-1.4.0+ds1/external/install/src/pufferfish/rank9b.cpp cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -pthread -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -c /build/salmon-1.4.0+ds1/src/FragmentLengthDistribution.cpp [ 76%] Linking CXX static library libpuffer.a cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/puffer.dir/cmake_clean_target.cmake cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/puffer.dir/link.txt --verbose=1 /usr/bin/ar qc libpuffer.a CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o CMakeFiles/puffer.dir/edlib.cpp.o CMakeFiles/puffer.dir/Util.cpp.o CMakeFiles/puffer.dir/rank9sel.cpp.o CMakeFiles/puffer.dir/rank9b.cpp.o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o CMakeFiles/puffer.dir/PufferfishStats.cpp.o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o CMakeFiles/puffer.dir/FastxParser.cpp.o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o CMakeFiles/puffer.dir/PufferFS.cpp.o CMakeFiles/puffer.dir/xxhash.c.o CMakeFiles/puffer.dir/FixFasta.cpp.o CMakeFiles/puffer.dir/MemCollector.cpp.o CMakeFiles/puffer.dir/MemChainer.cpp.o CMakeFiles/puffer.dir/PuffAligner.cpp.o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o /usr/bin/ranlib libpuffer.a make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 76%] Built target puffer [ 77%] Linking CXX static library libtwopaco.a cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/cmake -P CMakeFiles/twopaco.dir/cmake_clean_target.cmake cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/cmake -E cmake_link_script CMakeFiles/twopaco.dir/link.txt --verbose=1 /usr/bin/ar qc libtwopaco.a CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o CMakeFiles/twopaco.dir/constructor.cpp.o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o CMakeFiles/twopaco.dir/compressedstring.cpp.o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o CMakeFiles/twopaco.dir/test.cpp.o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o CMakeFiles/twopaco.dir/common.cpp.o /usr/bin/ranlib libtwopaco.a make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [ 77%] Built target twopaco [ 78%] Linking CXX executable unitTests cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/unitTests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/unitTests.dir/__/tests/UnitTests.cpp.o CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -o unitTests -L/build/salmon-1.4.0+ds1/lib -L/build/salmon-1.4.0+ds1/external/install/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" libalevin_core.a libsalmon_core.a -lgff /usr/lib/x86_64-linux-gnu/libstaden-read.so -lboost_iostreams -lboost_filesystem -lboost_system -lboost_timer -lboost_chrono -lboost_program_options -lboost_regex /usr/lib/x86_64-linux-gnu/libcurl.so -lz -lm -llzma -lbz2 -ltbb -ltbbmalloc -lgomp -lrt -ldl -pthread Copying unitTests cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E copy /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src/unitTests /build/salmon-1.4.0+ds1/tests/unitTests make[4]: 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-I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/Alevin.cpp.o -c /build/salmon-1.4.0+ds1/src/Alevin.cpp cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/SalmonQuantify.cpp.o -c /build/salmon-1.4.0+ds1/src/SalmonQuantify.cpp [ 92%] Building CXX object src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/WhiteList.cpp.o -c /build/salmon-1.4.0+ds1/src/WhiteList.cpp cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o -c /build/salmon-1.4.0+ds1/src/FragmentLengthDistribution.cpp cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o -c /build/salmon-1.4.0+ds1/src/FragmentStartPositionDistribution.cpp [ 93%] Building CXX object src/CMakeFiles/salmon.dir/GZipWriter.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/GZipWriter.cpp.o -c /build/salmon-1.4.0+ds1/src/GZipWriter.cpp In file included from /build/salmon-1.4.0+ds1/include/pcg_random.hpp:104, from /build/salmon-1.4.0+ds1/src/CollapsedGibbsSampler.cpp:23: /build/salmon-1.4.0+ds1/include/pcg_extras.hpp:563:51: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 563 | fnv(IntType(2166136261U ^ sizeof(IntType)), __DATE__ __TIME__ __FILE__); | ^~~~~~~~ /build/salmon-1.4.0+ds1/include/pcg_extras.hpp:563:60: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 563 | fnv(IntType(2166136261U ^ sizeof(IntType)), __DATE__ __TIME__ __FILE__); | ^~~~~~~~ In file included from /build/salmon-1.4.0+ds1/src/WhiteList.cpp:2: /usr/include/tbb/task_scheduler_init.h:21:154: note: '#pragma message: TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ [ 94%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o -c /build/salmon-1.4.0+ds1/src/SalmonQuantMerge.cpp [ 95%] Building CXX object src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o -c /build/salmon-1.4.0+ds1/src/ProgramOptionsGenerator.cpp [ 96%] Building CXX object src/CMakeFiles/salmon.dir/FASTAParser.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/FASTAParser.cpp.o -c /build/salmon-1.4.0+ds1/src/FASTAParser.cpp In file included from /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:65, from /build/salmon-1.4.0+ds1/include/AlevinUtils.hpp:46, from /build/salmon-1.4.0+ds1/include/Graph.hpp:8, from /build/salmon-1.4.0+ds1/src/Graph.cpp:1: /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h: In instantiation of 'T* spp::libc_allocator::reallocate(spp::libc_allocator::pointer, size_t) [with T = std::pair, unsigned int>; spp::libc_allocator::pointer = std::pair, unsigned int>*; size_t = long unsigned int]': /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:1383:38: required from 'void spp::sparsegroup::_set_aux(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&, spp::sparsegroup::realloc_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsegroup::allocator_type = spp::libc_allocator, unsigned int> >; spp::sparsegroup::size_type = unsigned char; spp::sparsegroup::realloc_ok_type = spp::integral_constant]' /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, spp::sparsegroup::size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsegroup::allocator_type = spp::libc_allocator, unsigned int> >; spp::sparsegroup::size_type = unsigned char]' /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsegroup::pointer = std::pair, unsigned int>*; spp::sparsegroup::value_type = std::pair, unsigned int>; spp::sparsegroup::allocator_type = spp::libc_allocator, unsigned int> >; spp::sparsegroup::size_type = unsigned char]' /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(spp::sparsetable::size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsetable::reference = std::pair, unsigned int>&; spp::sparsetable::value_type = std::pair, unsigned int>; spp::sparsetable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, spp::sparse_hashtable::size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::reference = std::pair, unsigned int>&; spp::sparse_hashtable::value_type = std::pair, unsigned int>; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, boost::hash > >::DefaultValue; KT = std::pair&; Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::value_type = std::pair, unsigned int>]' /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:3809:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::pair&; Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hash_map::mapped_type = unsigned int]' /build/salmon-1.4.0+ds1/src/Graph.cpp:10:29: required from here /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h:425:51: warning: 'void* realloc(void*, size_t)' moving an object of non-trivially copyable type 'struct std::pair, unsigned int>'; use 'new' and 'delete' instead [-Wclass-memaccess] 425 | pointer res = static_cast(realloc(p, new_size * sizeof(T))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/streambuf:41, from /usr/include/c++/10/bits/streambuf_iterator.h:35, from /usr/include/c++/10/iterator:66, from /usr/include/boost/graph/graph_traits.hpp:14, from /usr/include/boost/graph/depth_first_search.hpp:17, from /usr/include/boost/graph/connected_components.hpp:15, from /build/salmon-1.4.0+ds1/include/Graph.hpp:4, from /build/salmon-1.4.0+ds1/src/Graph.cpp:1: /usr/include/c++/10/bits/stl_pair.h:211:12: note: 'struct std::pair, unsigned int>' declared here 211 | struct pair | ^~~~ [ 97%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentModel.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/AlignmentModel.cpp.o -c /build/salmon-1.4.0+ds1/src/AlignmentModel.cpp [ 98%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o -c /build/salmon-1.4.0+ds1/src/SalmonQuantifyAlignments.cpp [ 99%] Building CXX object src/CMakeFiles/salmon.dir/BAMUtils.cpp.o cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-1.4.0+ds1/external -I/build/salmon-1.4.0+ds1/external/cereal/include -I/build/salmon-1.4.0+ds1/external/install/include -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon.dir/BAMUtils.cpp.o -c /build/salmon-1.4.0+ds1/src/BAMUtils.cpp /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::DropSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::DropSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2883:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::DropSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::DropSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2883:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CITESeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::CITESeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2899:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CITESeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::CITESeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2899:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::InDrop; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDrop; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDrop; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::InDrop; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2914:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::InDrop; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDrop; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDrop; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::InDrop; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2914:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::ChromiumV3; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::ChromiumV3; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2929:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::ChromiumV3; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::ChromiumV3; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2929:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::Chromium; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::Chromium; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2944:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::Chromium; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::Chromium; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2944:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::Gemcode; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::Gemcode; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2959:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::Gemcode; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::Gemcode; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2959:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ In file included from /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:65, from /build/salmon-1.4.0+ds1/include/AlevinUtils.hpp:46, from /build/salmon-1.4.0+ds1/include/Graph.hpp:8, from /build/salmon-1.4.0+ds1/include/DedupUMI.hpp:4, from /build/salmon-1.4.0+ds1/src/DedupUMI.cpp:1: /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h: In instantiation of 'T* spp::libc_allocator::reallocate(spp::libc_allocator::pointer, size_t) [with T = std::pair, unsigned int>; spp::libc_allocator::pointer = std::pair, unsigned int>*; size_t = long unsigned int]': /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:1383:38: required from 'void spp::sparsegroup::_set_aux(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&, spp::sparsegroup::realloc_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsegroup::allocator_type = spp::libc_allocator, unsigned int> >; spp::sparsegroup::size_type = unsigned char; spp::sparsegroup::realloc_ok_type = spp::integral_constant]' /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, spp::sparsegroup::size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsegroup::allocator_type = spp::libc_allocator, unsigned int> >; spp::sparsegroup::size_type = unsigned char]' /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsegroup::pointer = std::pair, unsigned int>*; spp::sparsegroup::value_type = std::pair, unsigned int>; spp::sparsegroup::allocator_type = spp::libc_allocator, unsigned int> >; spp::sparsegroup::size_type = unsigned char]' /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2251:27: required from 'void spp::sparsetable::move(spp::sparsetable::size_type, spp::sparsetable::reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsetable::size_type = long unsigned int; spp::sparsetable::reference = std::pair, unsigned int>&; spp::sparsetable::value_type = std::pair, unsigned int>]' /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2830:23: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2680:30: required from 'bool spp::sparse_hashtable::_maybe_shrink() [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >]' /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2846:13: required from 'void spp::sparse_hashtable::resize(spp::sparse_hashtable::size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hashtable::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:3795:51: required from 'void spp::sparse_hash_map::resize(spp::sparse_hash_map::size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hash_map::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:3797:41: required from 'void spp::sparse_hash_map::reserve(spp::sparse_hash_map::size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hash_map::size_type = long unsigned int]' /build/salmon-1.4.0+ds1/src/DedupUMI.cpp:39:36: required from here /build/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h:425:51: warning: 'void* realloc(void*, size_t)' moving an object of non-trivially copyable type 'struct std::pair, unsigned int>'; use 'new' and 'delete' instead [-Wclass-memaccess] 425 | pointer res = static_cast(realloc(p, new_size * sizeof(T))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/streambuf:41, from /usr/include/c++/10/bits/streambuf_iterator.h:35, from /usr/include/c++/10/iterator:66, from /usr/include/boost/graph/graph_traits.hpp:14, from /usr/include/boost/graph/depth_first_search.hpp:17, from /usr/include/boost/graph/connected_components.hpp:15, from /build/salmon-1.4.0+ds1/include/Graph.hpp:4, from /build/salmon-1.4.0+ds1/include/DedupUMI.hpp:4, from /build/salmon-1.4.0+ds1/src/DedupUMI.cpp:1: /usr/include/c++/10/bits/stl_pair.h:211:12: note: 'struct std::pair, unsigned int>' declared here 211 | struct pair | ^~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CELSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::CELSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2974:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CELSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::CELSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2974:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CELSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::CELSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2989:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CELSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::CELSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2989:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::QuartzSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::QuartzSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:3004:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::QuartzSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::QuartzSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:3004:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::Custom; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::Custom; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:3019:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::Custom; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::Custom; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:3019:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CustomGeometry; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::CustomGeometry; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:3023:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CustomGeometry; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2250:32: required from 'void do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2635:32: required from 'int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&) [with ProtocolT = alevin::protocols::CustomGeometry; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:3023:75: required from here /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:613:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 613 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ [100%] Linking CXX executable salmon cd /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/salmon.dir/EMUtils.cpp.o CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o CMakeFiles/salmon.dir/Salmon.cpp.o CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o CMakeFiles/salmon.dir/Graph.cpp.o CMakeFiles/salmon.dir/DedupUMI.cpp.o CMakeFiles/salmon.dir/Alevin.cpp.o CMakeFiles/salmon.dir/AlevinHash.cpp.o CMakeFiles/salmon.dir/SalmonAlevin.cpp.o CMakeFiles/salmon.dir/WhiteList.cpp.o CMakeFiles/salmon.dir/SalmonQuantify.cpp.o CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o CMakeFiles/salmon.dir/GZipWriter.cpp.o CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o CMakeFiles/salmon.dir/FASTAParser.cpp.o CMakeFiles/salmon.dir/AlignmentModel.cpp.o CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o CMakeFiles/salmon.dir/BAMUtils.cpp.o -o salmon -L/build/salmon-1.4.0+ds1/lib -L/build/salmon-1.4.0+ds1/external/install/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" ../external/pufferfish/src/libpuffer.a libsalmon_core.a ../external/pufferfish/external/twopaco/graphconstructor/libtwopaco.a ../external/pufferfish/external/twopaco/graphdump/libgraphdump.a ../external/pufferfish/external/ntcard/libntcard.a -lgff -lboost_iostreams -lboost_filesystem -lboost_system -lboost_timer -lboost_chrono -lboost_program_options -lboost_regex /usr/lib/x86_64-linux-gnu/libstaden-read.so /usr/lib/x86_64-linux-gnu/libcurl.so -lz -lm -llzma -lbz2 -lgomp ../external/pufferfish/src/libksw2pp.a libalevin_core.a -ljemalloc -ltbb -ltbbmalloc -lrt -ldl -pthread make[4]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' [100%] Built target salmon make[3]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' mv doc/source/license.rst doc/ # unused PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bhtml doc/source doc/build/html Running Sphinx v3.4.3 making output directory... done WARNING: html_static_path entry '_static' does not exist building [mo]: targets for 0 po files that are out of date building [html]: targets for 6 source files that are out of date updating environment: [new config] 6 added, 0 changed, 0 removed reading sources... [ 16%] alevin reading sources... [ 33%] building reading sources... [ 50%] file_formats reading sources... [ 66%] index reading sources... [ 83%] library_type reading sources... [100%] salmon /build/salmon-1.4.0+ds1/doc/source/alevin.rst:32: WARNING: Title underline too short. Providing multiple read files to Alevin ------------ /build/salmon-1.4.0+ds1/doc/source/alevin.rst:32: WARNING: Title underline too short. Providing multiple read files to Alevin ------------ /build/salmon-1.4.0+ds1/doc/source/alevin.rst:52: WARNING: Explicit markup ends without a blank line; unexpected unindent. /build/salmon-1.4.0+ds1/doc/source/alevin.rst:75: WARNING: Block quote ends without a blank line; unexpected unindent. /build/salmon-1.4.0+ds1/doc/source/alevin.rst:79: WARNING: Title overline too short. """""""""""" ``--whitelist`` """""""""""" /build/salmon-1.4.0+ds1/doc/source/alevin.rst:79: WARNING: Title overline too short. """""""""""" ``--whitelist`` """""""""""" /build/salmon-1.4.0+ds1/doc/source/alevin.rst:89: WARNING: Title overline too short. """""""""""" ``--noQuant`` """""""""""" /build/salmon-1.4.0+ds1/doc/source/alevin.rst:89: WARNING: Title overline too short. """""""""""" ``--noQuant`` """""""""""" /build/salmon-1.4.0+ds1/doc/source/alevin.rst:95: WARNING: Title overline too short. """""""""""" ``--noDedup`` """""""""""" /build/salmon-1.4.0+ds1/doc/source/alevin.rst:95: WARNING: Title overline too short. """""""""""" ``--noDedup`` """""""""""" /build/salmon-1.4.0+ds1/doc/source/alevin.rst:123: WARNING: Title overline too short. """""""""""" ``--dumpBfh`` """""""""""" /build/salmon-1.4.0+ds1/doc/source/alevin.rst:123: WARNING: Title overline too short. """""""""""" ``--dumpBfh`` """""""""""" /build/salmon-1.4.0+ds1/doc/source/alevin.rst:129: WARNING: Title overline too short. """""""""""" ``--dumpFeatures`` """""""""""" /build/salmon-1.4.0+ds1/doc/source/alevin.rst:129: WARNING: Title overline too short. """""""""""" ``--dumpFeatures`` """""""""""" /build/salmon-1.4.0+ds1/doc/source/alevin.rst:135: WARNING: Title overline too short. """""""""""" ``--dumpMtx`` """""""""""" /build/salmon-1.4.0+ds1/doc/source/alevin.rst:135: WARNING: Title overline too short. """""""""""" ``--dumpMtx`` """""""""""" /build/salmon-1.4.0+ds1/doc/source/alevin.rst:151: WARNING: Title overline too short. """""""""""""""""""""" ``--numCellBootstraps`` """""""""""""""""""""" /build/salmon-1.4.0+ds1/doc/source/alevin.rst:151: WARNING: Title overline too short. """""""""""""""""""""" ``--numCellBootstraps`` """""""""""""""""""""" /build/salmon-1.4.0+ds1/doc/source/alevin.rst:198: WARNING: Title underline too short. Output Quality Check ------------- /build/salmon-1.4.0+ds1/doc/source/alevin.rst:198: WARNING: Title underline too short. Output Quality Check ------------- /build/salmon-1.4.0+ds1/doc/source/alevin.rst:247: WARNING: Title underline too short. BibTex ---- /build/salmon-1.4.0+ds1/doc/source/alevin.rst:247: WARNING: Title underline too short. BibTex ---- /build/salmon-1.4.0+ds1/doc/source/alevin.rst:281: WARNING: Duplicate explicit target name: "swish". /build/salmon-1.4.0+ds1/doc/source/alevin.rst:281: WARNING: Footnote [#] is not referenced. /build/salmon-1.4.0+ds1/doc/source/alevin.rst:283: WARNING: Footnote [#] is not referenced. /build/salmon-1.4.0+ds1/doc/source/alevin.rst:285: WARNING: Footnote [#] is not referenced. /build/salmon-1.4.0+ds1/doc/source/alevin.rst:287: WARNING: Footnote [#] is not referenced. /build/salmon-1.4.0+ds1/doc/source/alevin.rst:289: WARNING: Footnote [#] is not referenced. /build/salmon-1.4.0+ds1/doc/source/alevin.rst:291: WARNING: Footnote [#] is not referenced. /build/salmon-1.4.0+ds1/doc/source/alevin.rst:293: WARNING: Footnote [#] is not referenced. /build/salmon-1.4.0+ds1/doc/source/alevin.rst:295: WARNING: Footnote [#] is not referenced. /build/salmon-1.4.0+ds1/doc/source/salmon.rst:2: WARNING: Duplicate explicit target name: "here". /build/salmon-1.4.0+ds1/doc/source/salmon.rst:2: WARNING: Duplicate explicit target name: "here". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 16%] alevin writing output... [ 33%] building writing output... [ 50%] file_formats writing output... [ 66%] index writing output... [ 83%] library_type writing output... [100%] salmon generating indices... genindex done writing additional pages... search done copying images... [100%] ReadLibraryIllustration.png copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 34 warnings. The HTML pages are in doc/build/html. mv doc/license.rst doc/source/ cd obj*/src && \ help2man --no-discard-stderr --no-info --name="highly-accurate, transcript-level quantification estimates from RNA-seq data"\ ./salmon > ../../debian/salmon.1 && \ for option in index quant swim; do help2man --no-discard-stderr \ --version-string="1.4.0+ds1" --no-info "./salmon --no-version-check ${option}" \ --include=../../debian/salmon-${option}-man-include \ > ../../debian/salmon-${option}.1; done make[1]: Leaving directory '/build/salmon-1.4.0+ds1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/salmon-1.4.0+ds1' dh_auto_test --no-parallel cd obj-x86_64-linux-gnu && make -j1 test ARGS\+=-j1 make[2]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process -j1 Test project /build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu Start 1: unit_tests 1/2 Test #1: unit_tests ....................... Passed 0.41 sec Start 2: salmon_read_test_quasi 2/2 Test #2: salmon_read_test_quasi ........... Passed 1.34 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 1.75 sec make[2]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/salmon-1.4.0+ds1' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/salmon-1.4.0+ds1' dh_auto_install cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/salmon-1.4.0\+ds1/debian/salmon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/salmon-1.4.0+ds1 -B/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/salmon-1.4.0+ds1/debian/salmon/usr/lib/libntcard.a -- Installing: /build/salmon-1.4.0+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets.cmake -- Installing: /build/salmon-1.4.0+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets-release.cmake -- Installing: /build/salmon-1.4.0+ds1/debian/salmon/usr/lib/libgraphdump.a -- Installing: /build/salmon-1.4.0+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets.cmake -- Installing: /build/salmon-1.4.0+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets-release.cmake -- Installing: /build/salmon-1.4.0+ds1/debian/salmon/usr/lib/libtwopaco.a -- Installing: /build/salmon-1.4.0+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets.cmake -- Installing: /build/salmon-1.4.0+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets-release.cmake -- Installing: /build/salmon-1.4.0+ds1/debian/salmon/usr/bin/salmon -- Installing: /build/salmon-1.4.0+ds1/debian/salmon/usr/lib/libsalmon_core.a Installation complete. Please ensure the following paths are set properly. ========================================================================== Please add /usr/bin to your PATH Please add /usr/lib to your LD_LIBRARY_PATH ========================================================================== make[2]: Leaving directory '/build/salmon-1.4.0+ds1/obj-x86_64-linux-gnu' rm -Rvf /build/salmon-1.4.0+ds1/debian/salmon/usr/lib removed '/build/salmon-1.4.0+ds1/debian/salmon/usr/lib/libsalmon_core.a' removed '/build/salmon-1.4.0+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets-release.cmake' removed '/build/salmon-1.4.0+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets.cmake' removed directory '/build/salmon-1.4.0+ds1/debian/salmon/usr/lib/twopaco' removed '/build/salmon-1.4.0+ds1/debian/salmon/usr/lib/libtwopaco.a' removed '/build/salmon-1.4.0+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets-release.cmake' removed '/build/salmon-1.4.0+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets.cmake' removed directory '/build/salmon-1.4.0+ds1/debian/salmon/usr/lib/graphdump' removed '/build/salmon-1.4.0+ds1/debian/salmon/usr/lib/libgraphdump.a' removed '/build/salmon-1.4.0+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets-release.cmake' removed '/build/salmon-1.4.0+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets.cmake' removed directory '/build/salmon-1.4.0+ds1/debian/salmon/usr/lib/ntcard' removed '/build/salmon-1.4.0+ds1/debian/salmon/usr/lib/libntcard.a' removed directory '/build/salmon-1.4.0+ds1/debian/salmon/usr/lib' make[1]: Leaving directory '/build/salmon-1.4.0+ds1' dh_installdocs dh_sphinxdoc dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'salmon' in '../salmon_1.4.0+ds1-1_amd64.deb'. dpkg-deb: building package 'salmon-dbgsym' in '../salmon-dbgsym_1.4.0+ds1-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../salmon_1.4.0+ds1-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2512877 and its subdirectories I: Current time: Sat Feb 11 22:02:08 -12 2023 I: pbuilder-time-stamp: 1676196128 Mon Jan 10 03:39:07 UTC 2022 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Mon Jan 10 03:39:07 UTC 2022 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Mon Jan 10 04:10:27 UTC 2022 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Mon Jan 10 04:10:27 UTC 2022 I: salmon_1.4.0+ds1-1_amd64.changes: Format: 1.8 Date: Thu, 26 Nov 2020 19:10:46 +0100 Source: salmon Binary: salmon salmon-dbgsym Architecture: amd64 Version: 1.4.0+ds1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: salmon - wicked-fast transcript quantification from RNA-seq data Changes: salmon (1.4.0+ds1-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.5.1 (routine-update) * debian/patches/portable_pause: remove, applied upstream * debian/patches/spelling: remove, applied upstream * debian/patches/include_fix: remove, applied upstream * Refreshed remaining patches * debian/control: build-dep on libsimde-dev, build for arm64 * debian/patches/spelling: new typo fixes Checksums-Sha1: 5af1519ebca41a62fdca0451438a8ed68ac26740 42884780 salmon-dbgsym_1.4.0+ds1-1_amd64.deb ee330937328d4475e71ae01a690f1086cf7910be 9866 salmon_1.4.0+ds1-1_amd64.buildinfo 50fdfeb5e236448ac0fe0cb30285767535316f63 2220920 salmon_1.4.0+ds1-1_amd64.deb Checksums-Sha256: 1421bbe87bee27246b39ceee608d69aeba1a88242566737a752ca880b8223074 42884780 salmon-dbgsym_1.4.0+ds1-1_amd64.deb 5c85a51b6a8c98ff96ad20604e31da5b48722da1299be2d5a18b47a6f0045f3c 9866 salmon_1.4.0+ds1-1_amd64.buildinfo e3444b52940b2dca4e00d7b1564a594e62242fe7136d44f708430abdf83afbbe 2220920 salmon_1.4.0+ds1-1_amd64.deb Files: 6f76a9ddb2d7f312aa8ab60c3655373c 42884780 debug optional salmon-dbgsym_1.4.0+ds1-1_amd64.deb 587628d8e87a9196b1f775ffdb5050ef 9866 science optional salmon_1.4.0+ds1-1_amd64.buildinfo 42bd2280850601437d8ee7ee2dc29ad5 2220920 science optional salmon_1.4.0+ds1-1_amd64.deb Mon Jan 10 04:10:28 UTC 2022 I: will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.VLIak0ug0A/salmon_1.4.0+ds1-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.VLIak0ug0A/salmon_1.4.0+ds1-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.VLIak0ug0A/salmon_1.4.0+ds1-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.VLIak0ug0A/b1/salmon_1.4.0+ds1-1_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.VLIak0ug0A/b2/salmon_1.4.0+ds1-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 1.359s) 1.359s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 1.092s) 1.092s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Jan 10 04:10:34 UTC 2022 I: found no differences in the changes files, and a .buildinfo file also exists. Mon Jan 10 04:10:34 UTC 2022 I: salmon from bullseye built successfully and reproducibly on amd64. Mon Jan 10 04:10:38 UTC 2022 I: Submitting .buildinfo files to external archives: Mon Jan 10 04:10:38 UTC 2022 I: Submitting 12K b1/salmon_1.4.0+ds1-1_amd64.buildinfo.asc Mon Jan 10 04:10:39 UTC 2022 I: Submitting 12K b2/salmon_1.4.0+ds1-1_amd64.buildinfo.asc Mon Jan 10 04:10:40 UTC 2022 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jan 10 04:10:40 UTC 2022 I: Done submitting .buildinfo files. Mon Jan 10 04:10:40 UTC 2022 I: Removing signed salmon_1.4.0+ds1-1_amd64.buildinfo.asc files: removed './b1/salmon_1.4.0+ds1-1_amd64.buildinfo.asc' removed './b2/salmon_1.4.0+ds1-1_amd64.buildinfo.asc'